Sea Urchin Research Articles

Crystal-Inspired Cellular Metamaterials and Triply Periodic Minimal Surfaces

Triply periodic minimal surfaces (TPMSs) are found in many natural objects including butterfly wings, sea urchins, and biological membranes. They simultaneously have zero mean curvature at every point and a crystallographic group symmetry. A metamaterial can be created from such periodic surfaces or used as a reinforcement of a composite material. While a TPMS as a mathematical object has been known since 1865, only novel additive manufacturing (AM) technology made it possible to fabricate cellular materials with complex TPMS shapes. Cellular TPMS-based metamaterials have remarkable properties related to wetting/liquid penetration, shock absorption, and the absence of stress concentrators. Recent studies showed that TPMSs are also found in natural crystals when electron surfaces are considered. Artificial crystal-inspired metamaterials mimic such crystals including zeolites and schwarzites. These metamaterials are used for shock, acoustic waves, and vibration absorption, and as structural materials, heat exchangers, and for other applications. The choice of the crystalline cell of a material, as well as its microstructure, plays a decisive role in its properties. The new area of crystal-inspired materials has many common features with traditional biomimetics with models being borrowed from nature and adjusted for engineering applications.

Phosphorylation-Dependent Regulation of Guanylyl Cyclase (GC)-A and Other Membrane GC Receptors.

Receptor guanylyl cyclases (GCs) are single membrane spanning, multidomain enzymes, that synthesize cGMP in response to natriuretic peptides or other ligands. They are evolutionarily conserved from sea urchins to humans and regulate diverse physiologies. Most family members are phosphorylated on four to seven conserved serines or threonines at the beginning of their kinase homology domains. This review describes studies that demonstrate that phosphorylation and dephosphorylation are required for activation and inactivation of these enzymes, respectively. Phosphorylation sites in GC-A, GC-B, GC-E and sea urchin receptors are discussed as are mutant receptors that mimic the dephosphorylated, inactive or phosphorylated, active forms of GC-A and GC-B, respectively. A salt bridge model is described that explains why phosphorylation is required for enzyme activation. Potential kinases, phosphatases and ATP regulation of GC receptors are also discussed. Critically, knock-in mice with glutamate substitutions for receptor phosphorylation sites are described. The inability of opposing signaling pathways to inhibit cGMP synthesis in mice where GC-A or GC-B cannot be dephosphorylated demonstrates the necessity of receptor dephosphorylation in vivo. Cardiac hypertrophy, oocyte meiosis, long bone growth/achondroplasia, and bone density are regulated by GC phosphorylation, but additional processes are likely to be identified in the future.

Divergence between sea urchins and their microbiota following speciation

Animals have a deep evolutionary relationship with microbial symbionts, such that individual microbes or an entire microbial community can diverge alongside the host. Here, we explore these host-microbe relationships in Echinometra, a sea urchin genus that speciated with the Isthmus of Panama and throughout the Indo-West Pacific. We find that the eggs from five Echinometra species generally associate with a species-specific bacterial community and that the relatedness of these communities is largely congruent with host phylogeny. Microbiome divergence per million years was higher in more recent speciation events than in older ones. We, however, did not find any bacterial groups that displayed co-phylogeny with Echinometra. Together, these findings suggest that the evolutionary relationship between Echinometra and their microbiota operates at the community level. We find no evidence suggesting that the associated microbiota is the evolutionary driver of Echinometra speciation. Instead, divergence between Echinometra and their microbiota is likely the byproduct of ecological, geographic, and reproductive isolations.

Circularity Assessment in Aquaculture: The Case of Integrated Multi-Trophic Aquaculture (IMTA) Systems

Circularity Assessment in Aquaculture: The Case of Integrated Multi-Trophic Aquaculture (IMTA) Systems

Trophic stability and change across a sea ice cover gradient on the western Antarctic Peninsula

The western Antarctic Peninsula (AP) is experiencing significant changes to sea ice cover, altering the macroalgal cover and potentially affecting the foundation of benthic food webs. We used fatty acid signatures as dietary and physiological trophic biomarkers to test the hypothesis that a gradient of 36-88% mean annual ice cover would affect the trophic ecology of fleshy macroalgae and diverse benthic invertebrate consumers along the western AP. We used SCUBA to collect organisms from benthic rocky nearshore habitats, 5-35 m depth, at 15 study sites during April-May of 2019. There were no consistent ecosystem-scale differences in the nutritionally important polyunsaturated fatty acids or other univariate fatty acid summary categories in either the seaweeds or invertebrates across the ice gradient, but we did find site-level differences in the multivariate fatty acid signatures of all seaweeds and invertebrates. Ice cover was a significant driver of the fatty acid signatures of 5 invertebrates, including 3 sessile (an anemone, a sponge, and a tunicate) and 2 mobile consumers (a sea star and a sea urchin). The multivariate fatty acid signatures of 2 other sea stars and a limpet were not affected by the ice gradient. These results indicate that the trophic ecology and resource assimilation of sessile consumers that are more connected to the macroalgal-derived food web will be more sensitive than mobile consumers to impending changes to annual ice and macroalgal cover along the western AP.

Inorganic UV filter-based sunscreens labelled as eco-friendly threaten sea urchin populations

Although the negative effects of inorganic UV filters have been documented on several marine organisms, sunscreen products containing such filters are available in the market and proposed as eco-friendly substitutes for harmful, and already banned, organic UV filters (e.g. octinoxate and oxybenzone). In the present study, we investigated the effects of four sunscreen products, labelled by cosmetic companies as “eco-friendly”, on the early developmental stages of the sea urchin Paracentrotus lividus, a keystone species occurring in vulnerable coastal habitats. Among sunscreens tested, those containing ZnO and TiO2 or their mix caused severe impacts on sea urchin embryos. We show that inorganic UV filters were incorporated by larvae during their development and, despite the activation of defence strategies (e.g. phagocytosis by coelomocytes), generated anomalies such as skeletal malformations and tissue necrosis. Conversely, the sunscreen product containing only new-generation organic UV filters (e.g. methylene bis-benzotriazolyl tetramethyl, ethylhexyl triazone, butylphenol diethylamino hydroxybenzoyl hexyl benzoate) did not affect sea urchins, thus resulting actually eco-compatible. Our findings expand information on the impact of inorganic UV filters on marine life, corroborate the need to improve the eco-friendliness assessment of sunscreen products and warn of the risk of bioaccumulation and potential biomagnification of inorganic UV filters along the marine food chain.

Effects of macroalgae and sea urchin grazing pressure on zoantharians growth under laboratory conditions

In the context of ocean warming, thermophilic organisms such as zoantharians are expanding and altering shallow benthic habitats. Here, a four-month laboratory experiment was performed to examine the influence of three types of macroalgae morphotypes common in the Canary Islands (turf algae, Lobophora spp., and crustose coralline algae) on the growth of two zoantharian species, Palythoa caribaeorum and Zoanthus pulchellus. Additionally, the grazing effects of echinoids Diadema africanum and Paracentrotus lividus were assessed as facilitators of substrate colonization by means of controlling macroalgae cover. Colony and algal coverages were measured at the beginning, middle and end of the experiment, and increments were calculated. Results indicated a general decrease in zoantharian colony sizes in contact with different algal types in the absence of sea urchins. However, P. caribaeorum colonies showed significant growth in the presence of D. africanum, highlighting the ecological importance of sea urchins in zoantharian population proliferation and subsequent community modification. This study represents the first investigation into zoantharian-macroalgae interactions under controlled conditions.

The stunting effect of an oxylipins-containing macroalgae extract on sea urchin reproduction and neuroblastoma cells viability

Different bioactive molecules extracted from macroalgae, including oxylipins, showed interesting potentials in different applications, from healthcare to biomaterial manufacturing and environmental remediation. Thus far, no studies reported the effects of oxylipins-containing macroalgae extracts on embryo development of marine invertebrates and on neuroblastoma cancer cells. Here, the effects of an oxylipins-containing extract from Ericaria brachycarpa, a canopy-forming brown algae, were investigated on the development of Arbacia lixula sea urchin embryos and on SH-SY5Y neuroblastoma cells viability. Embryos and cells were exposed to concentrations covering a full 0-100% dose-response curve, with doses ranging from 0 to 40 μg mL-1 for embryos and from 0 to 200 μg mL-1 for cells. These natural marine toxins caused a dose-dependent decrease of normal embryos development and of neuroblastoma cells viability. Toxicity was higher for exposures starting from the gastrula embryonal stage if compared to the zygote and pluteus stages, with an EC50 significantly lower by 33 and 68%, respectively. Embryos exposed to low doses showed a general delay in development with a decrease in the ability to calcify, while higher doses caused 100% block of embryo growth. Exposure of SH-SY5Y neuroblastoma cells to 40 μg mL-1 for 72 h caused 78% mortality, while no effect was observed on their neuronal-like cells derivatives, suggesting a selective targeting of proliferating cells. Western Blot experiments on both model systems displayed the modulation of different molecular markers (HSP60, HSP90, LC3, p62, CHOP and cleaved caspase-7), showing altered stress response and enhanced autophagy and apoptosis, confirmed by increased fragmented DNA in apoptotic nuclei. Our study gives new insights into the molecular strategies that marine invertebrates use when responding to their environmental natural toxins and suggests the E. brachycarpa’s extract as a potential source for the development of innovative, environmentally friendly products with larvicide and antineoplastic activity.

Post-synthetic modification of covalent organic framework for efficient adsorption of organochlorine pesticides from cattle's milk

Analysis of organochlorine pesticides (OCPs) residues in milk faces a significant challenge. Herein, a sea urchin structured covalent organic framework bearing boric acid groups named COF-B(OH)2 was synthesized and applied as a coating material for solid-phase microextraction (SPME) of the OCPs in cattle’s milk. Its performance was superior to that of three commonly used commercial SPME fibers, which could be due to the coexistence of hydrogen bonding, halogen bonding, π-stacking and electrostatic interactions. Besides, the fiber coating displayed good stability and reusability. After optimization, a COF-B(OH)2 based SPME coupled with gas chromatography-electron capture detection was established for the sensitive detection of the OCPs from milk samples. The limits of detection (S/N = 3) were between 0.04 and 1.0 μg kg−1. Satisfactory accuracy was achieved with the method recoveries in the range of 87.5 % to 112.5 %. These results manifest the feasibility of the COF-B(OH)2 coated fiber for the enrichment of the trace OCPs from milk samples.

Offshore oil and gas infrastructure plays a minor role in marine metapopulation dynamics

Decommissioning consequences of offshore oil and gas infrastructure removal on marine population dynamics, including connectivity, are not well understood. We modelled the connectivity and metapopulation dynamics of three fish and two benthic invertebrate species inhabiting the natural rocky reefs and offshore oil and gas infrastructure located in the Bass Strait, south-east Australia. Using a network approach, we found that platforms are not major sources, destinations, or stepping-stones for most species, yet act as modest sources for connectivity of Corynactis australis (jewel anemone). In contrast, sections of subsea pipelines appear to act as stepping-stones, source and destination habitats of varying strengths for all study species, except for Centrostephanus rodgersii (long-spined sea urchin). Natural reefs were the main stepping-stones, local source, and destination habitats for all study species. These reefs were largely responsible for the overall metapopulation growth of all study species (average of 96 % contribution across all species), with infrastructure acting as a minor contributor (<2 % average contribution). Full or partial decommissioning of platforms should have a very low or negligible impact on the overall metapopulation dynamics of the species explored, except C. australis, while full removal of pipelines could have a low impact on the metapopulation dynamics of benthic invertebrate species and a moderate impact on fish species (up to 34.1 % reduction in the metapopulation growth). We recommend that the decision to remove offshore infrastructure, either in full or in-part, be made on a platform-by-platform basis and consider contributions of pipelines to connectivity and metapopulation dynamics.

Spatial distribution of settlement of Diadema antillarum around Saba, Dutch Caribbean.

The mass mortality event of the herbivorous sea urchin Diadema antillarum in 1983-1984 has been a major contributor to the diminished resilience of coral reefs throughout the Caribbean. The reduction in grazing pressure resulted in algae proliferation, which inhibited coral recruitment after disturbances such as disease, hurricanes, pollution and climatic change induced marine heat waves. Natural recovery of D. antillarum after the 1983-1984 die-off has been slow. However, the few locations with recovered populations exhibit signs of improvement in coral reef health, prompting interest in D. antillarum restoration. Current restoration strategies include translocation of wild individuals, the restocking of juveniles that are either cultured from gametes or collected as settlers and head-started in a nursery, and assisted natural recovery by providing suitable settlement substrate. Both the collection of wild settlers and assisted natural recovery necessitate an understanding of the local, spatiotemporal trends in settlement. In this study, which was carried out on the Dutch Caribbean Island of Saba, artificial turf settlement collectors were deployed at nine locations around the island and monitored from June 2019 till July 2020 (13 months). The primary objective was to identify trends in larval settlement in space and time, to be able to optimize restoration efforts. Additionally, the small size of Saba allowed us to deploy settlement collectors around the island and compare D. antillarum settlement between windward and leeward sides. Our study showed that on Saba, D. antillarum settlement peaked in June and July, following similar seasonal trends observed around other islands in the Northeastern Caribbean. By far the most settlement occurred at the leeward side of the island, suggesting that hydrodynamic forces entrained D. antillarum larvae in the lee of Saba and/or calmer waters facilitated settlement. Limited settlement occurred on the more exposed windward locations. The identified high settlement locations are candidates for settler collection and restoration attempts. Continued monitoring of D. antillarum settlement, especially in light of the 2022 D. antillarum die-off, holds significance as it can provide insights into the potential of natural recovery.

Artificial light at night and warming impact grazing rates and gonad index of the sea urchin Centrostephanus rodgersii.

Artificial light at night (ALAN) is a growing threat to coastal habitats, and is likely to exacerbate the impacts of other stressors. Kelp forests are dominant habitats on temperate reefs but are declining due to ocean warming and overgrazing. We tested the independent and interactive effects of ALAN (dark versus ALAN) and warming (ambient versus warm) on grazing rates and gonad index of the sea urchin Centrostephanus rodgersii. Within these treatments, urchins were fed either 'fresh' kelp or 'treated' kelp. Treated kelp (Ecklonia radiata) was exposed to the same light and temperature combinations as urchins. We assessed photosynthetic yield, carbon and nitrogen content and C : N ratio of treated kelp to help identify potential drivers behind any effects on urchins. Grazing increased with warming and ALAN for urchins fed fresh kelp, and increased with warming for urchins fed treated kelp. Gonad index was higher in ALAN/ambient and dark/warm treatments compared to dark/ambient treatments for urchins fed fresh kelp. Kelp carbon content was higher in ALAN/ambient treatments than ALAN/warm treatments at one time point. This indicates ocean warming and ALAN may increase urchin grazing pressure on rocky reefs, an important finding for management strategies.

Recombinant SpTransformer proteins are functionally diverse for binding and phagocytosis by three subtypes of sea urchin phagocytes.

The California purple sea urchin, Strongylocentrotus purpuratus, relies solely on an innate immune system to combat the many pathogens in the marine environment. One aspect of their molecular defenses is the SpTransformer (SpTrf) gene family that is upregulated in response to immune challenge. The gene sequences are highly variable both within and among animals and likely encode thousands of SpTrf isoforms within the sea urchin population. The native SpTrf proteins bind foreign targets and augment phagocytosis of a marine Vibrio. A recombinant (r)SpTrf-E1-Ec protein produced by E. coli also binds Vibrio but does not augment phagocytosis. To address the question of whether other rSpTrf isoforms function as opsonins and augment phagocytosis, six rSpTrf proteins were expressed in insect cells. The rSpTrf proteins are larger than expected, are glycosylated, and one dimerized irreversibly. Each rSpTrf protein cross-linked to inert magnetic beads (rSpTrf::beads) results in different levels of surface binding and phagocytosis by phagocytes. Initial analysis shows that significantly more rSpTrf::beads associate with cells compared to control BSA::beads. Binding specificity was verified by pre-incubating the rSpTrf::beads with antibodies, which reduces the association with phagocytes. The different rSpTrf::beads show significant differences for cell surface binding and phagocytosis by phagocytes. Furthermore, there are differences among the three distinct types of phagocytes that show specific vs. constitutive binding and phagocytosis. These findings illustrate the complexity and effectiveness of the sea urchin innate immune system driven by the natSpTrf proteins and the phagocyte cell populations that act to neutralize a wide range of foreign pathogens.

Exploring indirect effects of a classic trophic cascade between urchins and kelp on zooplankton and whales

Kelp forest trophic cascades have been extensively researched, yet indirect effects to the zooplankton prey base and gray whales have not been explored. We investigate the correlative patterns of a trophic cascade between bull kelp and purple sea urchins on gray whales and zooplankton in Oregon, USA. Using generalized additive models (GAMs), we assess (1) temporal dynamics of the four species across 8 years, and (2) possible trophic paths from urchins to kelp, kelp as habitat to zooplankton, and kelp and zooplankton to gray whales. Temporal GAMs revealed an increase in urchin coverage, with simultaneous decline in kelp condition, zooplankton abundance and gray whale foraging time. Trophic path GAMs, which tested for correlations between species, demonstrated that urchins and kelp were negatively correlated, while kelp and zooplankton were positively correlated. Gray whales showed nuanced and site-specific correlations with zooplankton in one site, and positive correlations with kelp condition in both sites. The negative correlation between the kelp-urchin trophic cascade and zooplankton resulted in a reduced prey base for gray whales. This research provides a new perspective on the vital role kelp forests may play across multiple trophic levels and interspecies linkages.

Influence of physico-chemical parameters on the settlement of competent larvae of cultured sea urchin, Paracentrotus lividus

Achieving efficient metamorphosis and settlement of larvae is a major bottleneck in the culture of sea urchins; therefore, in order for culture operations to be economically viable, it is urgent to optimize this crucial step under captive conditions. This study aimed to investigate how various parameters, including temperature, salinity, light cycle, and inducer type, affect the settlement of competent P. lividus larvae. Three different salinities (35, 30, 25‰), three temperatures (25, 20, 15 °C), four light conditions (16/8, 12/12, 24/0 and 0/24) and five types of biofilms (three of “natural” origin and the other two from monospecific collection cultures) were tested. The results suggest a relationship between low salinity and decreased survival and settlement rates. Conversely, the photoperiod appears not to have significant influence over survival and settlement rates. It appears that specific temperatures did not affect rates of survival and settlement, rather it was the deviation from initial culture temperature that is responsible for these rates. Finally, the multispecific inoculum of benthic diatoms showed a higher survival and settlement rate and lower mortality rate compared to monospecific inoculum.

Transcription of microRNAs is regulated by developmental signaling pathways and transcription factors.

In early embryonic development, the cross-regulation of transcription factors and signaling pathways are critical in mediating developmental and physiological processes. Additionally, many studies have shown the importance of post-transcriptional regulation of signaling and network components mediated by microRNAs (miRNAs); however, how miRNAs are transcriptionally regulated is poorly understood. miRNAs are critical fine-tuners of many biological processes and their dysregulation leads to a variety of diseases and developmental defects. Previously, we have shown that miRNAs are dynamically expressed throughout sea urchin development, suggesting that miRNAs are likely to be under transcriptional regulation. Here, we used pharmacological inhibitors, genetic constructs, and loss-of-function reagents to assess the impact of key signaling pathways (Wnt, Nodal, MAPK, Sonic Hedgehog, Delta/Notch, VEGF, and BMP) and transcription factors (Alx1, Ets1/2, and Tbr) on the transcript levels of the evolutionarily conserved miR-1, miR-31, miR-92 and miR-124; the invertebrate-specific miR-71; and the echinoderm-specific miR-2002, miR-2007, and miR-2012. We also used computational methods to identify potential transcription factor binding sites of these miRNAs. Lists of binding motifs for transcription factors (TFs) were acquired from the MEME-Suite Motif Database and used as inputs for the algorithm FIMO (Find Individual Motif Occurrences), which detects short nucleotide motifs within larger sequences. Based on experimental data on miRNA expression in conjunction with bioinformatic predictions, we propose that the transcription factors Tbr, Alx1, and Ets1 regulate SpmiR-1, SpmiR-31, and SpmiR-71, respectively. We additionally observed significant effects on miRNA levels as a result of perturbations to Wnt, Nodal, MAPK, and Sonic Hedgehog signaling pathways, while no significant change on miRNA levels were observed with perturbations to Delta/Notch, VEGF, or BMP signaling pathways. Overall, this study provides insights into the transcriptional regulation of miRNAs by signaling pathways and transcription factors and contribute to our overall understanding of the genetic regulation of developmental processes.

Distribution of sea urchin barrens in shallow algal communities along the eastern Adriatic coast

The sea urchins Paracentrotus lividus and Arbacia lixula are important herbivores in algal communities of the infralittoral rocky bottoms in the Mediterranean Sea. However, grazing by sea urchins that outweighs natural algal recruitment processes might result in the formation of barrens, which are areas dominated by urchins and coralline algae. We present the results of the first large-scale mapping of sea urchin barrens and analyses of sea urchins’ impact on the main algal communities across 1955.5 km of rocky coastline on the eastern side of the Adriatic Sea (Croatia). Since mapping was performed over a geographically wide area and covered a representative quantity of approximately 40% of the coastline of the central part of the Adriatic Sea, the results could be considered to reflect the general situation in that area of the eastern Adriatic coast. Mapping revealed that sea urchin barrens are present along over 35% of the coastline, while the complete absence of algal cover was recorded in 8% of the inspected area. Communities with canopy-forming algae, which are the most valuable shallow-water communities of the Mediterranean Sea, represent the largest proportion of the observed coastline and are affected by sea urchins in over 28% of their extent. Among other factors, the extensive harvesting of date mussels (Lithophaga lithophaga) in the 1970s, 1980s, and early 1990s is likely one of the main activities that resulted in exceptional sea urchin expansion via the removal of micropredators and establishment of shelters for subadult urchins.

Effect of biodegradable polymers upon grazing activity of the sea urchin Paracentrotus lividus (Lmk) revealed by morphological, histological and molecular analyses

In the last years biodegradable polymers (BPs) were largely used as real opportunity to solve plastic pollution. Otherwise, their wide use in commercial products, such as packaging sector, is causing a new pollution alarm, mainly because few data reported about their behaviour in the environment and toxicity on marine organisms. Our previous results showed that embryos of the sea urchin Paracentrotus lividus (Lmk) exposed to poly(ε-caprolactone) (PCL), poly(3-hydroxybutyrate) (PHB) and poly(lactic acid) (PLA) showed delay of their development and morphological malformations, also affecting at the molecular levels the expression of several genes involved in different functional responses. In the present work for the first time, we tested the effects of five microplastics (MPs) obtained from BPs such as PBS, poly(butylene succinate), PBSA, poly(butylene succinate-co-butylene adipate), PCL, PHB and PLA, upon grazing activity of the sea urchin revealed by: i. histological analysis seeing at the gonadic tissues; ii. morphological analysis of the deriving embryos; iii. molecular analyses on these embryos to detect variations of the gene expression of eighty-seven genes involved in stress response, detoxification, skeletogenesis, differentiation and development. All these results will help in understanding how MP accumulated inside various organs in the adult sea urchins, and more in general in marine invertebrates, could represent risks for the marine environment.

Tracing the evolutionary origin of chordate somites in the hemichordate Ptychodera flava.

Metameric somites are a novel character of chordates with unclear evolutionary origins. In the early branching chordate amphioxus, anterior somites are derived from the paraxial mesodermal cells that bud off the archenteron (i.e., enterocoely) at the end of gastrulation. Development of the anterior somites requires FGF signaling, and distinct somite compartments express orthologs of vertebrate non-axial mesodermal markers. Thus, it has been proposed that the amphioxus anterior somites are homologous to the vertebrate head mesoderm, paraxial mesoderm and lateral plate mesoderm. To trace the evolutionary origin of somites, it is essential to study the chordates' closest sister group, Ambulacraria, which includes hemichordates and echinoderms. The anterior coeloms of hemichordate and sea urchin embryos (respectively called protocoel and coelomic pouches) are also formed by enterocoely and require FGF signals for specification and/or differentiation. In this study, we applied RNA-seq to comprehensively screen for regulatory genes associated with the mesoderm-derived protocoel of the hemichordate Ptychodera flava. We also used a candidate gene approach to identify P. flava orthologs of chordate somite markers. In situ hybridization results showed that many of these candidate genes are expressed in distinct or overlapping regions of the protocoel, which indicates that molecular compartments exist in the hemichordate anterior coelom. Given that the hemichordate protocoel and amphioxus anterior somites share a similar ontogenic process (enterocoely), induction signal (FGF), and characteristic expression of orthologous genes, we propose that these two anterior coeloms are indeed homologous. In the lineage leading to the emergence of chordates, somites likely evolved from enterocoelic, FGF-dependent, and molecularly compartmentalized anterior coeloms of the deuterostome last common ancestor.

Assembly of continuous high-resolution draft genome sequence of Hemicentrotus pulcherrimus using long-read sequencing.

The update of the draft genome assembly of sea urchin, Hemicentrotus pulcherrimus, which is widely studied in East Asia as a model organism of early development, was performed using Oxford nanopore long-read sequencing. The updated assembly provided ~600-Mb genome sequences divided into 2,163 contigs with N50 = 516 kb. BUSCO completeness score and transcriptome model mapping ratio (TMMR) of the present assembly were obtained as 96.5% and 77.8%, respectively. These results were more continuous with higher resolution than those by the previous version of H. pulcherrimus draft genome, HpulGenome_v1, where the number of scaffolds = 16,251 with a total of ~100 Mb, N50 = 143 kb, BUSCO completeness score = 86.1%, and TMMR = 55.4%. The obtained genome contained 36,055 gene models that were consistent with those in other echinoderms. Additionally, two tandem repeat sequences of early histone gene locus containing 47 copies and 34 copies of all histone genes, and 185 of the homologous sequences of the interspecifically conserved region of the Ars insulator, ArsInsC, were obtained. These results provide further advance for genome-wide research of development, gene regulation, and intranuclear structural dynamics of multicellular organisms using H. pulcherrimus.